Automated priming and library loading device
Inventors
AMINI, Sasan • Khaksar, Ramin • Taylor, Michael • Shokralla, Shadi • Haney, Christopher • Vaidyanathan, Pavan • POLLARD, Stephanie • Allred, Adam • Mortazavi, Sima • Tran, David • Namazi, Hossein • BARSI, Julius
Assignees
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Publication Number
US-11568958-B2
Publication Date
2023-01-31
Expiration Date
Abstract
Provided herein are automated apparatus and methods for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by library preparation and sequencing.
Core Innovation
The document describes microbiome/amplicon sequencing-based identification of microorganisms in food and environmental samples using targeted computational scanning of polymorphic gene regions to detect sequence variation independent of serotype. The targeted regions include SNP, RFLP, STR, VNTR, hypervariable/minisatellite/dinucleotide/trinucleotide/tetranucleotide repeats, indels, and insertion elements, and the scanning can also include epigenetic patterns such as methylation detection.
The approach uses predictive analysis that can classify organisms and support pathogenic versus non-pathogenic distinctions, including example organisms such as Salmonella, Campylobacter, Listeria, and Escherichia (E. coli). The computational scanning is applied to a fraction of sequencing data for high-sensitivity and high-specificity detection, and machine learning classification is used including SVM, random forest, logistic regression, and neural networks.
The document also describes predictive analytics for risk scoring and shelf-life prediction based on the detected microbial profiles. It further provides an automated nucleic-acid sequencing apparatus architecture intended to enable low/no-human-touch operation after loading, including a library preparation compartment with multiple chambers, a sequencing chamber with juxtaposed nanopore flow cells, automation/robotic handling, failure recovery by moving samples to an additional flow cell, and flow-cell reuse and re-priming concepts using distinct indexes/barcodes.
In addition, the document includes a specific automated nanopore flow-cell priming/loading device concept that uses a conditioning/liquid-filled sensor chamber, flow-path interruptions, and an alternative removable sample-input plug designed for robotic removal to enable fully automated priming and loading and on-demand re-priming/reuse.
Claims Coverage
The claims coverage is not explicitly described in patent, and no independent claims are identified in the provided items.
Not explicitly described in patent.
Stated Advantages
High-sensitivity detection and high-specificity detection of microorganisms independent of serotype.
Computational scanning enables classification using a predictive scanning fraction of sequencing data.
Association of sequencing results with food processing facilities using barcodes or molecular indices.
Predictive risk assessment, including shelf-life prediction.
Low/no-human-touch operation after loading enabled by automated library preparation and sequencing apparatus architecture.
Failure recovery by rerouting samples to additional nanopore flow cells.
Flow-cell reuse and re-priming concepts using distinct indexes or barcodes.
Fully automated priming and loading enabled by the conditioning/liquid-filled sensor chamber, flow-path interruptions, and a robotic-removable sample-input plug.
Documented Applications
Identification of microorganisms in food samples and environmental samples such as surface swab/rinse and equipment/clothing.
Microorganism detection for distinguishing pathogenic versus non-pathogenic organisms, with examples including Salmonella, Campylobacter, Listeria, and Escherichia (E. coli).
Linking microbial identification results to food processing facilities using barcodes or molecular indices.
Risk scoring and shelf-life prediction based on microbial detection and predictive analytics.
Automated nanopore sequencing workflow using automated library preparation and nanopore flow-cell priming/loading and reuse for low/no-human-touch operation after loading.
Detecting epigenetic patterns, including methylation patterns, from food and environmental samples.
Detecting pathogens from food and environmental samples.
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