I know it is not a fungus, but it, like other bacteria and several fungi can be isolated from skin scrapings. Even Pseudomonas can be found in lesions, (which, of course, can be very pathogenic). All of these bacteria and fungi are found naturally in soil. They only become pathogenic when a horse's immune system and skin health allow it to.
5cc of injectable vitamin A given orally is far from a toxic dose. Since it is stored in the liver, a horse can store a lot of it without any toxic reactions. It would have to be dosed in huge quantities over a long period of time to see any problems. The feed supplement we recommed once a horse has been started on Vitamin A is Farnam's Mare Plus. If a horse is on a daily grain ration, it is easy to feed it. Not so much when horses are run out in large groups.
It was first recommended to me by a nutritionist with a PhD in livestock nutrition that worked for the Moorman Mineral Company. He also started me supplementing Calcium, Magnesium and Zinc to horses on grass hay. I got very sound advice from him and have followed it for more than 40 years with nothing but excellent results. After addressing dietary issues, I never again had a foal born with weak or crooked legs, never had any breeding problems if infections were not present, never had to 'clean' another mare and had fewer eye problems like goopy, crusty eyes. Does it not seem strange that all of these problems show up in horses in poor condition or well-cared for horses in the winter and spring months when hay has lost its Vitamin A and there is no green grass? Obviously it would be best if a horse could get all of the Vitamin A they needed from their natural diet. Winter stops that -- but then it also stops them from having foals out of season. There is a 'natural' reason for mares to stay out of any fertile heats until there is green grass and they are naturally shedding. This is the same time that they start getting sufficient Vitamin A again.
He showed ranchers and dairymen how to keep calves healthy, how to get optimum healthy growth from calves and foals, how to get cows to breed back consistently in 60 days or less after calving, how to avoid Milk Fever and most importantly, how to keep Vet bills down. I wish I had 'picked his brain' more than I did because he never led me wrong. The Moorman Mineral Company was faaar ahead of their time. There is a reason that the Vets where I used to live sent all of their tough re-hab cases to me that they did not want to bother with. [I also used to run all of the bacterial cultures for the local Vet clinic back then, bred several mares for the Vets, and collected stallions and did semen evaluations for them back then.]
You can keep treating and re-treating Rain Rot cases all you want, but if you add 100,000 IU units of Vitamin A to a horse's daily diet, you will never have to treat another one. BUT, there is a lot less money to be made preventing it and treating it with diet like it should be addressed than selling toxic substances to kill it. .