2024 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized) v2

Version Updates v5: Added links to GalaxyTrakr_PT_exercise_report_2022.xlsx v6: added 2023 PT strains; edited Steps 1, 2, 4, and 5 to include references to growth of Listeria on BHIA plates; Updated Tables in Steps 7.1 and 8.1 with sample information for 2023 PT strains. v7: Section 9 and Section 11: deleted file GalaxyTrakr_PT_exercise_report_2023.xlsx; uploaded new file version GalaxyTrakr_PT_exercise_report_2023-v2.xlsx v8: Added new guidelines for the 2024 PT exercise including strain identifiers for the 2024 isolates, steps for processing Camyplobacter isolates, links for sample processing and data quality assessment protocols. Removed requirements to submit spreadsheet containing output from GalaxyTrakr This SOP outlines guidelines on how to process the isolates for the 2024 GenomeTrakr (GT) Proficiency Testing exercise. This SOP is applicable to all GenomeTrakr labs participating in the 2024 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized). The FDA GenomeTrakr program will ship the following proficiency testing isolates in April 2024. ESP24-4709: Escherichia coli SAP24-0369: Salmonella enterica SAP24-0005: Salmonella enterica CAP24-7320: Campylobacter jejuni Completion of the entire proficiency test entails the following: GT participating laboratory generates sequencing data (fastq files) using the PT strains provided by CDC through FDA-CFSAN-WGS Program-GT in accordance to GT and/or PulseNet SOPs. Populate sample sheet according to 2024GT Proficiency Testing exercise (PulseNet Harmonized) SOP Submission of sequencing records to the appropriate project on BaseSpace or Isilon according to GT SOPs By participating in the 2024 GT Proficiency Testing exercise (PulseNet Harmonized), GT labs provide consent to use the PT exercise data in subsequent analysis and manuscript publications. Participants will be acknowledged for their contribution on any publication that might require processing data from the 2024 GT PT exercise.