Hello I am Dr. Joey. Thanks for trusting me to help you and your pet today. I am a licensed veterinarian with over 15 years of experience. I look forward to working with you. I apologize for the delay in an expert responding to you.
Sounds like so far your two vets have done a good job looking for the normal causes of this type of issue. If only the kitten was affected then at this point I would be concerned we either have an atypical infectious problem (infectious such as atypical parasite or infection are most common) or her digestive tract is just terribly upset from the initial insult and needs some help stabilizing. I did not see that she is on a probiotic. If not, then this is a definite must right now; she may need this for several weeks. There are several options for this. The two made for pets that I trust are Fortiflora or Proviable. For people you could try Culturelle (half capsule daily or use one of the child's caps once daily) or VSL#3 (this is more expensive and you would be doing about half a capsule). This helps tremendously to normalize the system. Sounds like you have already done a bland diet (such as Hills i/d or Purina En or Eukanuba Low residue) for a few weeks, and this would help to continue.
I recognize you have spent a lot of money already but if you and your vet were to do a next step test it would be to submit the comprehensive stool sample to the lab to have a PCR test for all the infectious diseases like campylobacter, giardia, tritrichomonas, etc. I do think it important to have your vet do a cytology evaluation of the stool but for them to report no "bacteria" suggests this was done. As well, an X-ray may be helpful to ensure this is not due to her having swallowed something that is stuck in her system. However, with the other cat affected, an infectious cause (parasites, bacteria) becomes more likely.
I do want to comment on the no response to metrondazole which is a highly effective anti-diarrheal. This may indicate again one of the atypical infections like campylobacter which can be contagious between cats and is not very responsive to this medication. You could always discuss doing a trial with the treatment antibiotic for this (there are two choices can try for this) and doing a general dewormer (if not already done) with a 5-day panacur course.
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