Purpose: In this study, whole-genome sequence (WGS) data from a set of Salmonella Agona isolates were analyzed to provide insight into the evolutionary relationships among strains linked to two outbreaks of salmonellosis separated by ten years.
Methods: We analyzed WGS sequence data from 46 Salmonella Agona isolates. Five out of 46 isolates were associated with the 1998 outbreak and 25 isolates were associated with the 2008 outbreak while 16 isolates were unrelated to both events. We reconstructed a phylogenetic hypothesis of the samples using a reference-free k-mer based method for identifying variable sites. We then tested alternative hypothesis regarding differences in mutation rates and historical fluctuations in effective population size.
Results: Using SNP analyses, we were able to distinguish and separate Salmonella Agona isolates from both outbreaks with only a few SNP differences between them. The phylogeny illustrates that the 2008 outbreak involves direct descendants from the 1998 outbreak rather than a second independent contamination event. Estimates of historical fluctuations in population size for the whole dataset and one reduced to only containing the isolates associated with the outbreak showed that the latter had little to no change in effective population size. Further, there are fewer numbers of SNP differences within genes linked to cell mobility, intracellular transport, and transcription within the cereal clade.
Significance: Based on these results, there is evidence supporting the persistence of Salmonella over time with little genomic changes and that emerging lineages or clonal swarms may harbor a higher mutational load than observed in the larger population.