Location: Characterization and Interventions for Foodborne Pathogens
Title: Investigations into Nanopore-based sequencing for portable detection of foodborne pathogens: Simulation, detection limit, and quantificationAuthor
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Gehring, Andrew |
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Armstrong, Cheryl |
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Capobianco Jr, Joseph |
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Counihan, Katrina |
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Harper, Sky |
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Kanrar, Siddhartha |
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Paoli, George |
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Tilman, Shannon |
Submitted to: Meeting Abstract
Publication Type: Abstract Only Publication Acceptance Date: 1/10/2025 Publication Date: N/A Citation: N/A Interpretive Summary: Technical Abstract: Six hundred million cases of disease and roughly 420,000 deaths occur globally each year due to foodborne pathogens. Current methods to screen and identify pathogens in cattle, poultry, and swine products include immuno-based techniques (e.g., immunoassay integrated biosensors), molecular methods (e.g., DNA hybridization and PCR assays), and traditional culturing. Current detection methods employed by the United States Department of Agriculture’s Food Safety and Inspection Service require several days to identify prominent foodborne pathogenic bacteria (e.g., at least 4 days for Shiga-toxin Producing E. coli or STEC and 6 days for Listeria monocytogenes). Adoption of long-read, whole genome sequencing for food safety testing could significantly reduce the time needed for identification, but method development costs are currently high. Multiple criteria (e.g., accuracy, precision, rapidity, cost, robustness, etc.) are required for the acceptance of new analytical methods. This presentation will focus on elucidation of the minimum detectable level and quantification criteria associated with the application of nanopore-based, long-read sequencing using the MinION platform Oxford Nanopore Technologies) intended for field-portable detection of foodborne bacterial pathogens. Results of in-silico and in-vitro research will demonstrate that although the sequencing technology may be proven to be accurate, relatively rapid, and portable, it currently is not practically capable of low level detection of “zero tolerance,” food-associated bacteria without the co-application of culture enrichment. However, the technology does hold promise for quantification of targeted bacteria in the presence of significantly higher amounts of background microbial flora. |