Mixed solid waste is transported from a waste collection vehicle to a first room of a waste treatment facility. The first room defines an enclosed isolation zone that is configured to receive the mixed solid waste from the waste collection vehicle. The mixed solid waste is treated in at least one process vessel in the first room to destroy a majority of pathogens in the mixed solid waste to yield a sanitized waste. The sanitized waste is transported to a second room of the facility. The second room defines a clean zone that is separated from the first room by a barrier.