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A system for treating infectious waste is provided that employs a medical waste handling and shredding sub-system that feeds partially processed waste to an oxidizer to eliminate potential airborne infectious waste prior to transforming the medical waste into useful co-products. Medical waste is transformed into value added products including hydrocarbon based gases, hydrocarbon-based liquids, carbonized material, and recovered precious metals and rare earth materials in a system having as its transformative element an anerobic, negative pressure, or carbonization system. With medical waste as a feedstock for the production of valuable products, an economically viable and environmentally more responsible alternative to traditional methods of medical waste treatment is realized.