Please disregard the auto-call offer, as its from the site not myself. And you are welcome to post a photo when you can.
Now I cannot see any mention of how long you have been back from holiday. Though the reason I asked was because while stress can impact their stools and their health generally, to see it with you home suggests this isn't just stress. It may have dampened her immune system but to see signs continue once all is back to normal at home usually is a sign that bacterial (sometimes viral or parasitic) infections gaining a foot hold. And for her to have increased respiratory noise rings alarm bells of a brewing airway infection, so the Baytril is not unreasonable here and the stool sample is spot on to look for infectious causes for the loose stools.
That said, one issue that does concern me is your mention of her struggles with the pepper. This is because we can see situations where their molars overgrow leading to difficulity eating. And when that happens they can selective graze (eating less hay and leaning to softer foods) which could in turn could affect stool quality and her weight. As well, if she is loose with her stools, there will be nutrient loss there from reduced gut absorption and that too will negatively impact Ebony's weight. So, we'd want her teeth checked if the vets have not done so already.
Furthermore, besides what has been dispensed, we need her vets putting her on a probiotic to support her good gut bacteria. This will help with the stools but also reduce any gas from pathogenic bacteria (a concern if she is hunched up as that tends to be a sore gut sign in this species). There are a range of cavy probitoics that can be used but as her stools aren't formed, you can have her vet dispense Fibreplex to firm them as well as support the good bacteria. Plus increase her dietary fiber. If she isn't eating a good amount of hay, use canned pumpkin (from the International aisle in most big grocery stores), veggie baby food, etc. as those will bulk up stool too. And if you are modifying her diet, make sure spinach isn't given in abundance since its too calcium rich and can cause bladder stones for this species. And if she isn't drinking well, you can flavour her water with low sugar fruit juice of you can syringe feed fluids (aim for 4.8ml per 100 g of her weight daily).
Finally, I am keen to see her neck if you can post a photo. The treatments she is on should help with an abscess or soft tissue inflammation, but I have to note that we could also be seeing this from her blood proteins being too low (as they lose protein with diarrhea and when the blood proteins drop, fluid leaks into places like under the jaw, belly, or legs) or secondary to tooth root abscesses (though usually hard unless there is secondary infection). So, we'd want to keep an eye on that but would hope that as they treat and as we reduce the looseness in her stools that will settle; else an xray may be the next step for Ebony.
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