I am no real expert on Lyme Disease, but I have done a lot of research. This is my understanding of how the vaccine works based on that research.
Lyme is caused by a type of bacteria called a spirochete, which means it is corkscrew shaped. The Lyme bacteria have proteins on their surface known as Outer Surface Proteins or Osp's. The Osp's are named alphabetically, for example, Osp A, Osp B, Osp C, etc. These proteins change depending on where the bacteria is. When the bacteria is inside the tick, it is coated with Osp A. When the tick feeds on an animal and the bacteria is transferred from the tick into the animal, the surface proteins change from Osp A to Osp C. During the acute stage of Lyme Disease, Osp C is most prevalent. As the infection becomes chronic, they alter to Osp F.
The way the vaccine works is that, rather than targeting the bacteria directly, it targets Osp A. This is why it may work against the many different strains of Lyme bacteria. It is also why the vaccine is not always as effective as we would wish, it is targeting a surface protein that may not always be present and is constantly changing.
The way that the Lyme bacteria change their outer surfaces is also one of the reasons that the animal's immune system has such a difficult time dealing with Lyme bacteria. The immune system gears up and produces antibodies to attack Osp A or C, but by the time they are ready, the Osp has changed to F and the antibodies can't find the bacteria.
The corkscrew shape of the bacteria also plays a role in this because they burrow or "screw" themselves into parts of the body that are generally safe from bacterial attack. The immune system has many ways to attack intruders in the digestive tract or the skin, but not so much in the sealed off portions of the body. It is not as well equipped to deal with these kind of attacks and often has to fight back in unusual ways, which is why the symptoms of Lyme are so varied and difficult to pin down.
In trying to reach these hidden bacteria, the immune system may make an all out, inflammatory response that is difficult to turn off after it has done its job. This all-out immune response is one of the things that makes people and animals so sick. This kind of response is very similar to an autoimmune reaction where the body actually attacks itself.
Unfortunately, such an all out response is difficult to stop once it has been triggered and may contribute to lingering effects of Lyme Disease. While it is controversial, many believe that "Chronic Lyme" is in fact an autoimmune reaction that is triggered by the Lyme disease and then becomes impossible to stop, even after the bacteria are all killed. While it is possible to treat Lyme disease, autoimmune diseases cannot be treated.
There is some evidence, again controversial, that people and animals do develop a degree of immunity after infection and successful treatment. However, there are many, many strains of Lyme so it is possible to get Lyme disease, get treated successfully and then get reinfected with a different strain the next time you walk outdoors.
Many horses have pretty severe reactions to tick bites. They often develope a rash around the bite and I have seen numerous skin abscesses caused by bites. Usually, bites occur in areas where it is impossible to tell if the rash is circular (such as under the chin or groin area) and I would never have seen the bullseye on Emma were it not for a quirk of grey color genetics. The hair of grey or roan equines often grows back either lighter or darker after an injury, which is what happens here....
Emma lost all the hair in this circular area last year when she had this rash. However, she did not lose the hair all at once, it came out in patches over the course of several weeks. Her new undercoat grew back darker than the rest because she is a dapple grey with a tendency for small wounds to grow back in darker than her normal coat. It is the only reason that it is visible. A similar rash occurring on Tessa or Ramsey would never be visible this way because their hair would grow back the same color, which is what makes me wonder just how often a bullseye rash actually occurs in animals.
I have yet to find any real way of preventing tick bites. I have tried just about every concoction I have ever heard of, from herbal to toxic poison. None of them work. I check my animals and myself every day, but I know I miss some. Tessa always gets a rash when she gets bitten and it is often this rash that tells me I missed another one.
All the animals are vaccinated and I have to have some faith in it, if only for my peace of mind, but it is a wary faith. The vaccine will not do anything for the other tick borne diseases that are becoming nearly as prevalent.
My only suggestion is to do everything you can and have a SNAP test done at the least hint that someone is having a bad day. The SNAP test is fairly cheap, about $30, and easy. It tests for Lyme, anaplasmosis, eherliciosis, and heart worm in dogs and cats. If you have a positive test, treat the animal. Many vets won't treat unless they see obvious symptoms. However, the signs are so often subjective and hard to see until after treatment, that I disagree with this practice. Every animal I have seen with a positive test who got treated showed marked improvement. Usually, the owners didn't even know they were seeing symptoms of disease until after they were gone.
I hope that this has answered some of the questions. I neglected to write them all down and now I can't find them online. If I missed any, let me know.