No genus&species prediction for Salmonella enterica subsp. arizonae (or diarizonae) #2
Description
Came across a Salmonella enterica (supposedly subspecies arizonae or diarizonae) sample from a partner where GAMBIT did not assign a genus/species due to the matched.distance_threshold's being set to 0
The top 10 ref genome matches were 10 different genomes called "Salmonella enterica subspecies 2", so I would have expected GAMBIT to confidently assign the genus and species.
We're not entirely sure if this sample belongs to the IIIa subspecies (arizonae) or IIIb subspecies (diarizonae) as seqsero2 and SISTR were undecided but both pointed in this direction
Here's a review on Salmonella enterica nomenclature with more explanation of the subspecies https://www.sciencedirect.com/science/article/pii/S0944501317304159
Can share a link to the Terra workspace privately.
This is low priority to fix, but might be good to update the GAMBIT database & thresholds in case labs do sequence these rare/uncommon Salmonella enterica samples and run them through GAMBIT (a la TheiaProk workflows)