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Muscle aches and pains (myalgias) may be caused by any one of a number of things but are a common feature of infections, especially those that result in fever. Both the elevated temperatures and the inflammation in the muscles indicate that some of the bacteria, or its toxins, have gotten into the bloodstream. This should continue to improve with the antibiotics. If not, you should see your doctor again for a re-evaluation.
Myalgias may or may not be a feature of an infection. They might also be the result of strenuous activity. Certain medications, including those used for high cholesterol, can cause pain in the large muscles of the body. Viruses are on the list. Fibromyalgia is a poorly understood autoimmune disease that is marked by muscle pain. Some individuals have more than one reason simultaneously. Regardless of the cause, anti-inflammatories such as ibuprofen and naproxyn tend to work a lot better than tylenol which does not address the inflammation.