Short term use of antibiotics for bacterial conditions is appropriate when a known or suspected organism is causing a disorder. Good medicine dictates that the antibiotic be specific for the organism(s). If there is no improvement in symptoms in the first 48 hours, a culture of the infection should be taken to isolate the organism and adjust the antibiotic to one that is specific for that strain of bacteria. Rarely, a disorder will be identified that necessitates the use of long term-antibiotic therapy. Your vet should be able to tell why this decision is necessary and educate you about the disorder.
Antibiotics are actually designed to help the immune system do its job, and it may do that in the short term, but in the long term antibiotics actually suppress the immune system. Chronic use of antibiotics may wind up harming the immune system. The immune system is actually a collection of defensive mechanisms against disease, and includes certain tissues, organs, cells, and enzymes. These elements work together to create a disease fighting system more powerful than anything medicine has yet to devise. Even the biggest breakthrough in fighting viruses in medical history, the vaccine, is simply a way to help the natural immune system do its job better.
The immune system functions just like an organ or a muscle. When it is not put to use, it atrophies. So when an introduced agent does one its jobs, the immune system performs that job poorly once the agent leaves the body.
Antibiotics also do not make the distinction between harmful bacteria and helpful bacteria and cells. They "throw the baby out with the bathwater" so to speak. Certain strains of bacteria in the digestive tract are essential to digest food and produce healthy vitamins. When these bacteria are killed off, it may lead to vitamin loss, diarrhea, parasitic infection, and the development of allergies.
