Bacterial Infection vs. Virus: What is the Difference?

The mare was sick. Her temperature was 103.0 F, heavy mucus hung from her nostrils, discharge came from her eyes, her appetite was poor and a cough was developing. 
"Can you give her an antibiotic?" asked the owner. "It won't work - she doesn't have a bacterial infection. The tests show she has influenza, which is a virus." replied the vet. "It will have to run it's course."

Bacteria? Virus?
What is the difference?
Bacteria are living organisms. They are composed of a single cell. Bacteria can live and reproduce without a host. Many types survive extreme heat or cold…even radioactive waste. 
There are "good" and "bad" forms of bacteria.  Good bacteria are essential to life. In the digestive system beneficial bacteria aid in the utilization of nutrients in food. Other examples of good bacteria are: the yeast in bread which allows it to rise, the bacteria in penicillin that enables it to help healing and the bacteria found on the roots of legumes (peas, alfalfa, peanuts, etc.) that allows those plants to grow. 
Unfortunately there is also bad bacteria. Many can cause illness. A few examples of equine diseases caused by bad bacteria are: botulism (Clostridium botulinum), strangles (Streptococcus equi), tetanus (Clostridium tetani) and Lyme disease (Borrelia burgdorferi).
Antibiotics have been developed that can kill certain types of bacteria. But antibiotics also kill the good bacteria within the body, and overuse of antibiotics can create resistant bacterial strains.
Viruses are parasites. They need a host cell to survive and reproduce. There are specific viruses that attack specific cells. Some forms attack bacteria.
Examples of equine diseases caused by a virus are: Eastern equine encephalitis, equine rhinovirus, vesicular stomatitis and equine influenza.
Antibiotics do not kill viruses and treatment of viral infections is difficult. Supporting the body through good care and watching for secondary infections, while waiting for the disease to subside, are the only options.
Quarantine of the sick horse and consulting a veterinarian is warranted, whether the horse is battling a bacteria or virus. Identification of the disease will give you the tools to help the horse.
Consult your veterinarian about a vaccination schedule. Vaccinations can help protect your horse from specific viral and bacterial equine diseases.