There are many classifications of pathogens such as viral, protozoa, bacteria, viruses and parasites. Each are different in their approaches and it is important to focus on this. The only thing you have at the moment is a positive for citrobacter farmeri which is a gram negative bacteria, this is a pathogen, thus will make you sick. This approach would be different than say a parasite.
One of the keys is understanding the term Antibiotic sensitivity. This means there are a bunch of different antimicrobial substances and you have to find the right substance to kill what you have. Because substance 1 may kill pathogenA, does not mean substance 1 will kill pathogenB. I am surprised that your doctors do not know this, this is basic science.
If you do indeed have citrobacter farmeri then you should focus the treatments to this. Gram negative bacteria are more difficult to get rid of than gram positive and this is due to the membrane structure of the bacteria.
I do know that collodial silver can kill gram negative. Buy resultsrna ACS200 which has been tested to kill more than others (and no, I have no affiliation with them)> https://amzn.to/2zOZD6K
Oftentimes, it is better to use a wide spectrum approach, this gives you a better chance. There are other natural Antibiotics that I know that have a potential to kill gram negatives. I can list out if you would like them.