Is she drooling while resting calmly? Is she swallowing weird for no apparent reason? Like there's phlegm in there? Or turning her head grimacing when trying to lay down or when getting UP quickly? Is she doing any of that in the early morning?
I ask because besides pain and anxiety, that's also a rule in for nausea and acid reflux...and a differential diagnosis would be gastric bacteria from contaminated water. That's what my dog had, Helicobacter Pylori (HP) which turns into bleeding gastric ulcers and more. Much more - IBD, esophagitis, motility problems, megaesophagus. It can get really bad and even sudden death, albeit he had a long line of symptoms including puking yellow bile. He died from it. And he very likely had it for alot longer time than Brandy possibly has, she could be in early stages. So it's not that obvious. Now, if she were stray BEFORE Lori had her and adopted her out, then she could have been carrying it around for longer like my Rocky, neglected living out in a yard with dirty water then stray on the streets, too.
HP is common worldwide but lays dormant until you get sick/immune compromised then it's a nightmare of a thing to get rid of sometimes and it's very opportunistic. The number one cause of ulcers in humans (and dogs).
There is no way to dx that in dogs without a scope which should only be done for life saving measures and
way too dangerous for her anyway. Sometimes getting scope can cause irreparable damage. So IF she is tolerating the treatment I'd ask about Helicobacter treatment in conjunction with the Lyme - or after. If they think she can do it health wise.
It's called "triple therapy" Dr. Marshall's protocol =
two specific antibiotics (Doxi is not one of them, unfortunately) with an acid inhibitor like Prevacid.
If she's regurgitating mucous/bile/anything or vomiting then you add Carafate to protect the gi system from the acid reflux burn which you assume she has in that regurge. Then it's called quadruple therapy. You MUST be very compliant with the Carafate directions and follow them explicitly when they tell you to not give it a certain amount of time before or after other food, water or meds. OTHERWISE it binds them up and causes a blockage. Carafate coats the GI tract to prevent burn and also binds to the bleeding ulcer tissue to kill and break it off as it is getting resolved from the antibiotics. So you don't want it to BIND to other materials.
I would make sure she gets a
probiotic with the antibiotic (Doxi most likely?) and all the vets I know lately are using this one:
Amazon.com: Purina Veterinary Diets Fortiflora Canine, 30 Sachets Per Box: Pet Supplies
Since Doxi only has a 22% resolution rate for Helicobacter Pylori, I'd STRONGLY consider prophylactic antibiotic treatment for Helicobacter (gastritis etc) using Dr. Marshall's protocol of the higher rated antibiotics that are proven to resolve HP better (whenever they think she's up to it depending on her Lyme protocol, symptoms and strength). Her vet will know what I'm talking about if they are an experienced vet, NOT A RESIDENT. The story of Dr. Marshall and his life changing discovery of HP is famous. I think by now they have a combo RX packet for it with both correct antibiotics together from what I remember. You just add a PPI or another specific choice of an acid inhibitor. When my dog had it there was no such thing specifically for HP at the time just knowledge and RX the "right" A/Bs. And it was a mess, he couldn't swallow pills and was foaming/vomiting/regurging up all the liquid forms we tried. Except the Carafate because that has no bitter flavor it's just like a small amount of chalky water. IF she starts regurging/puking ACT FAST.
Stomach Infection with Helicobacter in Dogs | petMD
I'm sure Lori knows how to read her body language really well but sometime people mistake the signs of the gi disorder when there's no diarrhea for behavioral. But yes, pain is a rule in for HP, too. And sometimes dogs exhibit pain as anxiety. In a dog like her with this trauma they get all mixed in together.
I hope she has a peaceful, speedy recovery.