Location: Meat Safety and Quality
Project Number: 3040-42000-020-018-T
Project Type: Trust Fund Cooperative Agreement
Start Date: May 1, 2024
End Date: Apr 30, 2025
Objective:
The Objective Is to review 4 Salmonella outbreaks by comparing the core genome and non-core genome variation using the USMARC relatedness pipeline.
Approach:
We will receive information about four Salmonella foodborne outbreaks from members of the meat industry. We will then find the Salmonella isolates in the National Center for Biotechnology Information’s (NCBI) Pathogen Detection Isolates Browser (PDIB) to look at relatedness amongst isolates. Genomic data will be downloaded from NCBI and analyzed using the newly developed genomic relatedness pipeline developed at USMARC. The analysis pipeline will use the core genes on the chromosome to look at relatedness of isolates and compare them to the results from the PDIB analysis. The variable genome will be analyzed using the USMARC pipeline by mapping sequencing reads to a closed reference genome from the related outbreak cluster. This will show if there are DNA fragments inserted into the genome or deleted from the genome. The unmapped reads will be assembled to see if there are additional DNA fragments that are not represented in the genome. These results will allow a complete genomic comparison of the relatedness of isolates within each outbreak cluster.
