x
- Do the 4 clinical isolates (ASM_26, ASM_31, ASM_49, and ASM_50) that are epidemiologically linked to eggs from state #2 match any of the environmental or food swabs collected at those facilities?
The four outbreak isolates (highlighted in yellow) are closely related to, but do not match exactly to, food or environmental swaps in these facilities
- Do any of the remaining 19 clinical isolates match clinical isolates from question #1? Do they match any of the food or environmental isolates? Are there additional clinical clusters?
The remaining 19 clinical isolates (highlighted in green) have exact (or nearly identical) matches to food or envrionment swaps, with the exceptions of ASM41, ASM42, ASM44, and ASM45, which have no close environmental or food-derived relatives
- Are there other clinical Salmonella isolates in public databases (including, but not limited to, samples from BioProjects PRJNA237212, PRJNA227458, PRJNA252015, and PRJNA230403) that match food or environmental isolates collected at these facilities in these two states?
All isolates differ greatly from the randomly chosen reference genome. We have yet to identify the phylogenetic relatedness to the four posted reference genomes or other genomes in NCBI databases
Results by other groups: a, b