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What Does An Infectious Disease Doctor Treat? Infectious disease specialists treat a wide variety of acute and chronic medical infections and diseases. In the hospital setting, ID doctors commonly treat polymicrobial infections (infections involving more than one organism). Common bacterial infections may be caused by Staph aureus, Escherichia coli and Pseudomonas aeruginosa. Bacterial infections can involve the bone (osteomyelitis), heart valves (endocarditis), blood (bacteremia) or prosthetic surgery implants. Other infections may be caused by viral or fungal organisms. Fungal infections can either be acute or chronic such as blastomycosis and aspergillosis. In clinics, ID specialists primarily treat chronic conditions such as HIV and hepatitis but may also follow up with previously hospitalized patients and see patients with lingering conditions or sub-acute infections.