Q Do any of these lineages have known anti-microbial resistance genes?
Yes, they all do!
Q Are our new sequences (SRR19310037, SRR19310038, and SRR19127720) closely related in the ML tree?
Nope!
Q Are our new sequences (SRR19310037, SRR19310038, and SRR19127720) closely related in the bootstrap consensus tree?
Also no
Q What do these relationships suggest about if this is a new outbreak cluster, or endemic variation?
These seem to be from endemic varaition.
Q Does changing the reference taxon change the sequences?
Yes! 119 bases are different calls, and there are many gaps and or ambiguities that are not shared.
Q Does changing the reference taxon change the phylogeny or inferences you would make from it?
Nope!