Food borne illness outbreak investigations require accurate genotyping to identify outbreak clusters and link them to isolates recovered from possible sources of infection. Traditional genotyping methods such as PFGE lack the resolution to differentiate highly similar but epidemiologically unrelated isolates. Single Nucleotide Polymorphism (SNP) analysis of whole genome sequences shows promise in providing the required level of resolution, but lacks field relevant data to aid interpretation of results. Here, three E. coli strains of serotypes commonly associated with foodborne illness outbreaks were used to inoculate lettuce growing under field conditions and recovered weekly for SNP analysis. This pilot study indicates that the number of SNP differences accumulated in these strains while growing under field relevant conditions is very low, but that variability exists between strains and further study is warranted. These results will aid interpretation of SNP analyses during food outbreak investigations and help support resulting regulatory decisions.
Keywords: Single Nucleotide Polymorphisms (SNPs); foodborne illness outbreak investigation; genotyping; genomic based comparison; Enterohemorrhagic E. coli (EHEC); field relevant.