Whole genome sequencing (WGS) has become in the last decade the gold standard subtyping method for foodborne pathogens. Salmonella, Listeria, E. coli, and Campylobacter are among some of the foodborne pathogens for which isolates are routinely sequenced. Sequence data are submitted to a centralized database and available back to Departments of Health through different tools (e.g., SEDRIC), which can be used for comparison of isolates as part of cluster investigations or outbreak responses. This curriculum aims to provide (i) foundational knowledge needed to understand the genetics and genomics of microbial organisms, as well as the WGS data, how it is acquired and processed; (ii) intermediary knowledge regarding how WGS data is used to generate outputs, such as allele codes, phylogenetic trees and single nucleotide polymorphism (SNP) distance matrices, data visualization using SEDRIC, epi-lab communication; and (iii) advanced knowledge on specific topics (e.g., allele X codes, REP strains) that may present additional challenges to surveillance and outbreak investigation.
Registration: https://cals.cornell.edu/whole-genome-sequencing-curriculum