Abstract: The present invention provides methods for managing livestock to improve performance and health of the general livestock population by reducing the impact of subclinical animals persistently infected with a contagious disease by separating animals into arrival groups, screening all animals for the pathogen of the contagious disease, promptly removing the pathogen positive animals from the general livestock population and feeding and managing the pathogen negative animals and pathogen positive animals separately. In preferred embodiments, the pathogen positive animals are removed from their arrival group within about 1.5-3 days after arrival. In preferred embodiments, the method of the present invention is applied in a cattle operation such as a seedstock operation, a cow-calf operation, a stocker operation, a backgrounding operation, a feedlot operation, a dairy operation, a farm of origin, such as a dairy farm, an auction facility, a gathering point or a buyer facility.