detection-and-isolation-of-campylobacter-spp-from-raw-meat

Detection and Isolation of <i>Campylobacter </i> spp. from Raw Meat 

This article presents a rapid yet robust protocol for isolating Campylobacter spp. from raw meats, specifically focusing on Campylobacter jejuni and ...

Agricultural Research Service (ARS), United States Department of Agriculture (USDA)

Shiga toxin-producing  (STEC) and  are routinely responsible for severe foodborne illnesses in the United States. Current identification methods utilized by the U.S. Food Safety Inspection Service require at least four days to identify STEC and six days for . Adoption of long-read, whole genome sequencing for food safety testing could significantly reduce the time needed for identification, but method development costs are high. Therefore, the goal of this project was to use NanoSim-H software to simulate Oxford Nanopore sequencing reads to assess the feasibility of sequencing-based foodborne pathogen detection and guide experimental design. Sequencing reads were simulated for STEC, , and a 1:1 combination of STEC and  genomes using NanoSim-H. At least 2500 simulated reads were needed to identify the seven genes of interest targeted in STEC, and at least 500 reads were needed to detect the gene targeted in . Genome coverage of 30x was estimated at 21,521, and 11,802 reads for STEC and , respectively. Approximately 5-6% of reads simulated from both bacteria did not align with their respective reference genomes due to the introduction of errors. For the STEC and  1:1 genome mixture, all genes of interest were detected with 1,000,000 reads, but less than 1x coverage was obtained. The results suggested sample enrichment would be necessary to detect foodborne pathogens with long-read sequencing, but this would still decrease the time needed from current methods. Additionally, simulation data will be useful for reducing the time and expense associated with laboratory experimentation.

Katrina Counihan

Characterization and Interventions for Foodborne Pathogens Research Unit,
Eastern Regional Research Center,
Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center

Agricultural Research Service (ARS), United States Department of Agriculture (USDA)

Detection and Isolation of Campylobacter spp. from Raw Meat

Katrina Counihan

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Agricultural Research Service (ARS), United States Department of Agriculture (USDA)

Detection and Isolation of Campylobacter spp. from Raw Meat

Characterization and Interventions for Foodborne Pathogens Research Unit,
Eastern Regional Research Center,
Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center