Purpose: Strain evaluations were performed to determine the evolutionary relationship of strains collected during multiple SFPO.
Methods: Genome sequences were produced using the Illumina MiSeq desktop sequencer. After quality filtering, de novo assemblies were constructed for downstream analyses, which included phylogenetic estimation based on a SNP matrix and also on a concatenated alignment of core genes. Core genes and functional differences were determined based on identifying orthologous genes from PGAP annotations of the de novo assemblies.
Results: Gene concurrence was observed at 96.2%, based on WGS and PCR results. The phylogenetic relationships among the outbreak samples indicated a strong degree of population substructure where many well-supported clades were found. These clades tended to be best explained by collection date. Analyses of homologous genes revealed that the core genome was substantially smaller (n=132) than the average number of open reading frames found within each sample (n=2706). We also found that the evolutionary history of many genes was indicative of recombination/horizontal gene transfer, which provides further support for the fluidity of S. aureus genomes.
Significance: The recovery of enterotoxigenic multi-resistant strains and the persistence of staphylococcal strains on food industry surfaces may result in food contamination which is a serious risk for consumers. The results presented here illustrate the utility of WGS data to provide information on fine scale population genetic structure, genomic differences among phenotypically different strains, and the role that temporal dynamics has in shaping those patterns.