Sorry you are going through all of this! My thought is that if it is Crohn's you will know it eventually. There are a lot of bacterial infections and imbalances that don't show up on stool cultures. It might be a good idea for your doc to try treating you with antibiotics to see if it will clear things up for you. If that doesn't work it might be helpful if your doc is willing to try a tapering dose of Prednisone, just to see if that will settle things down. Post infectious irritable bowel is a real thing. Even after antibiotics it can take a long time for the IBS symptoms to settle down
I have Crohn's disease that we believe has been in remission since bowel resection surgery in 2014. Nevertheless, I have endless problems with bacterial infections and SIBO (small intestine bacterial overgrowth) Sometimes things show up on stool cultures and sometimes it doesn't. I do understand the lack of sleep from bowel issues! Currently we are trying one week of Flagyl a month and three weeks off. We are going to do this for three months to see if we can re-set the SIBO issues. Probiotics have never helped me, but do seem to help others.
The current belief is that Crohn's is caused by both genetic and environmental factors and a bad bowel infection seems to trigger Crohn's for people susceptible to it. This is a very frustrating disease, and my guess is that the inflammation and bowel damage from Crohn's has different causes for different people, which makes it even harder to treat.
My best advice is to try to find a GI doctor that will keep working with you to try to help you control symptoms and re-test if you are not getting better.
59 yr. old female, diagnosed with Crohn's in terminal ileum Sept-Oct. 2007. Dx. with c.difficile 1/12, 10/14, 11/15, 1/16. Fecal transplant on 2/24/16, and so far, no more c.diff!
5/20/14: Ileo-colic resection surgery after stricturing and partial bowel obstruction.
Not currently on any Crohn's meds and in remission, but struggling with bad IBS.