Single nucleotide polymorphisms reveal the genetic relatedness of Staphylococcus aureus isolates within food outbreaks
Investigation of bacterial food poisoning outbreaks by whole genome sequencing can rely on the inspection of the genetic relatedness among isolates through the application of single nucleotide polymorphisms (SNPs) thresholds. However, no consensus exists for Staphylococcus aureus. In this study we proposed an SNP cutoff by taking into account the mutation rate and the evolution time. Through in vitro microevolution we determined the mutation rate of isolates grown under mimicked food stressing conditions. Compared to INDELs and structural rearrangements, SNPs were the most frequent mutations and increased under stress compared with standard laboratory conditions. From the mutation rate we set a cutoff value of 28 SNPs considering 30 days as evolution time based on the average shelf-life of foods contaminated by S. aureus and the timeline for identifying pathogens in outbreaks. The SNP threshold was applied to retrospectively study ten staphylococcal food outbreaks in order to assess whether or not two or more isolates from the same outbreak could be considered as genetically linked. To support the SNP threshold, we used the phylogenetic tree topology. In most cases we observed that isolates differing by up to 28 SNPs were displaying a monophyletic relationship. Our suggested cutoff can be used to identify S. aureus strains as identical or not in outbreak management.