Septic arthritis can be caused by bacterial, viral or fungal infections. Bacterial infection with Staphylococcus aureus (staph) is the most common cause. Staph commonly lives on even healthy skin.
Septic arthritis may develop when an infection elsewhere in your body, such as an upper respiratory tract infection or urinary tract infection, spreads through your bloodstream to a joint. Less commonly, a puncture wound, drug injection or surgery in or near a joint may give the germs a pathway into the joint space.
The lining of your joints (synovium) has little ability to protect itself from infection. Your body's reaction to the infection — including inflammation that can increase pressure and reduce blood flow within the joint — contributes to the damage.
Source: http://www.mayoclinic.com